WASHINGTON — Not long after American forces defeated the Iraqi government of Saddam Hussein in 2003, caravans of trucks began to arrive at Andrews Air Force Base outside Washington on a regular basis, unloading an unusual cargo — pallets of shrink-wrapped $100 bills.

​The cash, withdrawn from Iraqi government accounts held in the United States, was loaded onto Air Force C-17 transport planes bound for Baghdad, where the Bush administration hoped it would provide a quick financial infusion forIraq’s new government and the country’s battered economy.

Over the next year and a half, $12 billion to $14 billion was sent to Iraq in the airlift, and an additional $5 billion was sent by electronic transfer. Exactly what happened to that money after it arrived in Baghdad became one of the many unanswered questions from the chaotic days of the American occupation, when billions were flowing into the country from the United States and corruption was rampant.

Finding the answer became first the job and then the obsession of Stuart W. Bowen Jr., a friend from Texas of President George W. Bush who in 2004 was appointed to serve as a special inspector general to investigate corruption and waste in Iraq. Before his office was finally shut down last year, Mr. Bowen believed he might have succeeded — but only partly — in that mission.

Much of the money was probably used by the Iraqi government in some way, he concluded. But for years Mr. Bowen could not account for billions more until his investigators finally had a breakthrough, discovering that $1.2 billion to $1.6 billion had been stolen and moved to a bunker in rural Lebanon for safe keeping. “I don’t know how the money got to Lebanon,” Mr. Bowen said. “If I knew that, we would have made more progress on the case.”

Mr. Bowen kept the discovery and his investigation of the cash-filled bunker in Lebanon, which his office code-named Brick Tracker, secret. He has never publicly discussed it until now, and his frustration that neither he nor his investigators can fully account for the missing money was evident in a series of interviews. “Billions of dollars have been taken out of Iraq over the last 10 years illegally,” he said. “In this investigation, we thought we were on the track for some of that lost money. It’s disappointing to me personally that we were unable to close this case, for reasons beyond our control.”

He is equally frustrated that the Bush administration, apart from his office, never investigated reports that huge amounts of money had disappeared, and that after his investigators found out about the bunker, the Obama administration did not pursue that lead, either. Mr. Bowen said his investigators briefed the C.I.A. and the F.B.I. on what they found. But Mr. Bowen added that he believed one reason American officials had not gone after it was “because it was Iraqi money stolen by Iraqis.”

Spokesmen for the F.B.I. and C.I.A. declined to comment for this article.

The Iraqi government has also not tried to retrieve the money, and has kept information about the Lebanese bunker secret. Mr. Bowen said that he talked to Prime Minister Nuri Kamal al-Maliki about the missing money and his discovery of the bunker and that Mr. Maliki never took any action, while expressing anger at the way the United States had handled the airlifted cash.

The money so assiduously carried to Iraq from a vast facility in New Jersey operated by the Federal Reserve Bank of New York came from the Development Fund of Iraq, which was created by a United Nations resolution in May 2003 to hold Iraqi oil revenue. The fund was to be used in Iraq’s reconstruction, and the United Nations resolution called for the creation of a monitoring board to make sure the United States-led Coalition Provisional Authority, which governed Iraq in 2003 and the first half of 2004 and ordered the cash flights, used the money properly for the benefit of the Iraqi people.

For the C.P.A., an advantage of using the cash from the Development Fund instead of money appropriated by Congress for Iraq was that there were not a lot of rules governing its use, and no federal regulations or congressional oversight of what happened to it. It was Iraqi money, not anything from American taxpayers.

In an interview, Paul Bremer, who was the head of the C.P.A., defended the agency’s handling of the funds, and said the money was badly needed to keep Iraqi government ministries in operation. In particular, he defended the decision to accelerate the cash flights in June 2004, just before the provisional authority closed and was replaced by an interim Iraqi government. In the last two weeks of June, the C.P.A. ordered $4 billion to $5 billion in cash to be flown to Baghdad from New York in a rapid-fire series of last-minute flights.

The Iraqi government “was broke at that point,” Mr. Bremer said. “Civil servants had not been paid for about three months. We had to get funds there right away.” He said that there was a budget process in Baghdad that determined how much cash was requested from the Federal Reserve.

“The issue is what happened to the money once it was distributed through the minister of finance,” he said. “We had a very clear record of funds going to the Iraqi system.”

Mr. Bowen was dismissive of Mr. Bremer’s defense of the C.P.A. Accounting for the funds was so lax, he said, that there were few credible records of how it was spent. “Our auditors interviewed numerous senior advisers of the C.P.A., and we learned from them that the controls on the Development Fund of Iraq money were inadequate,” Mr. Bowen said. “We didn’t make this up; we learned this from C.P.A. staff.”

Former Treasury Department officials also questioned the need for the flights. Treasury had already sent $1.7 billion in cash from Iraqi government accounts in the United States to Baghdad in the first weeks after the invasion, and then had developed a new Iraqi currency that was introduced that October. They say the new currency ended the need for further cash infusions from the United States.

“We did not know that Bremer was flying in all that cash,” said Ged Smith, who was the head of the Treasury Department team that worked on Iraq’s financial reconstruction after the invasion. “I can’t see a reason for it.”

Mr. Bowen said that Brick Tracker, his office’s most sensitive investigation, began in 2010 when Wael el-Zein, a Lebanese- American on his staff, received a tip about stolen money hidden in Lebanon. An informant told him about the bunker, which in addition to the cash, was believed to also have held approximately $200 million in gold belonging to the Iraqi government.

But by this time, official Washington had long since forgotten about the flights from Andrews. The C.I.A. expressed little interest in pursuing the matter, and the F.B.I. said it lacked jurisdiction, Mr. Bowen recalled. And when Mr. Bowen and his staff tried to conduct an investigation of the missing cash in Lebanon, they also met with resistance from the United States Embassy in Beirut.

Mr. Bowen was not allowed to travel to Lebanon on official business. Two of his investigators who did travel to Lebanon were denied permission from the embassy to see the bunker themselves because it was too dangerous. When Mr. Bowen’s staff members met in Beirut with Lebanon’s prosecutor general, Said Mirza, he initially agreed to cooperate on an investigation, but later decided against it.

The office of the special inspector general for Iraq closed in 2013, and Mr. Bowen is now working in the private sector. Mr. Bowen thinks at least some of the money has been moved, and said it is impossible to say whether any of it is still in the bunker. He says he is still frustrated by the lack of cooperation he got from his own government in his efforts to pursue the missing cash. “We struggled to gain timely support from the interagency as we pursued this case,” Mr. Bowen said.

This article is adapted from “Pay Any Price: Greed, Power and Endless War” by James Risen, to be published Tuesday by Houghton Mifflin Harcourt.